<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_1/emdb.xsd" version="3.0.9.1" emdb_id="EMD-26010">
    <admin>
        <current_status>
            <date>2024-01-17</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-01-21</deposition>
            <header_release>2022-03-09</header_release>
            <map_release>2022-03-09</map_release>
            <update>2024-01-17</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>S10OD021600</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>P41GM103832</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>R01GM079429</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>P01GM121203</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of Mental Health (NIH/NIMH)</funding_body>
                <code>R21MH125285-01A1</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>The symmetrized subpellicular microtubule map from intact Toxoplasma gondii cells</title>
        <authors_list>
            <author ORCID="0000-0001-9004-8494">Sun SY</author>
            <author ORCID="0000-0003-1311-7868">Chen M</author>
        </authors_list>
        <keywords>parasites, Toxoplasma gondii, cytoskeleton, microtubules, CELL INVASION</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0001-9004-8494" order="1">Sun SY</author>
                    <author ORCID="0000-0003-4151-5513" order="2">Segev-Zarko LA</author>
                    <author order="3">Chen M</author>
                    <author order="4">Pintilie GD</author>
                    <author ORCID="0000-0003-1077-5750" order="5">Schmid MF</author>
                    <author ORCID="0000-0002-1903-1574" order="6">Ludtke SJ</author>
                    <author order="7">Boothroyd JC</author>
                    <author ORCID="0000-0002-8910-3078" order="8">Chiu W</author>
                    <title>Cryo-ET of Toxoplasma parasites gives subnanometer insight into tubulin-based structures.</title>
                    <journal_abbreviation>Proc.Natl.Acad.Sci.USA</journal_abbreviation>
                    <country>US</country>
                    <volume>119</volume>
                    <year>2022</year>
                    <external_references type="PUBMED">35121661</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.2111661119</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>In situ subpellicular microtubule of Toxoplasma gondii</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>In situ subpellicular microtubule of Toxoplasma gondii</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="5811">Toxoplasma gondii</organism>
                </natural_source>
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.2</ph>
                        <details>Hanks balanced salts solution, supplemented (HBSS): 1 mM MgCl2, 1 mM CaCl2, 10 mM NaHCO3, 20 mM HEPES, pH 7.2</details>
                    </buffer>
                    <grid>
                        <model>Homemade</model>
                        <material>COPPER</material>
                        <mesh>200</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>LACEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>PLASMA CLEANING</type>
                            <time units="s">25</time>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">295</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                    </vitrification>
                    <details>3x10^6 cells/ml</details>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI TALOS ARCTICA</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">1.0</nominal_defocus_max>
                    <nominal_magnification>39000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <specialist_optics>
                        <phase_plate>VOLTA PHASE PLATE</phase_plate>
                        <energy_filter>
                            <name>GIF Bioquantum</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <average_electron_dose_per_image units="e/Å^2">2.2</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="Å">80.0</delta_z>
                            <delta_phi units="deg">27.7</delta_phi>
                            <axial_symmetry>C13</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">26.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>1994</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>10</number_tomograms>
                    <number_images_used>1994</number_images_used>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
                    </software_list>
                </extraction>
                <final_angle_assignment>
                    <type>OTHER</type>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3539">
        <file>emd_26010.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>96</col>
            <row>96</row>
            <sec>96</sec>
        </dimensions>
        <origin>
            <col>-48</col>
            <row>-48</row>
            <sec>-48</sec>
        </origin>
        <spacing>
            <x>96</x>
            <y>96</y>
            <z>96</z>
        </spacing>
        <cell>
            <a units="Å">680.256</a>
            <b units="Å">680.256</b>
            <c units="Å">680.256</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-6.0420027</minimum>
            <maximum>7.9477882</maximum>
            <average>0.06696106</average>
            <std>0.84975946</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">7.086</x>
            <y units="Å">7.086</y>
            <z units="Å">7.086</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-26010::::</label>
    </map>
</emd>
